The research was conducted using climbing perch samples originated from the swampy waters of the southern Borneo, and the objektive of this study to investigate the genetic diversity and the conservation aspect using mtDNA amplification method. mtDNA amplification process occurs in the D Loop region. The results of the analysis of D-Loop mtDNA of climbing perch showed that, the analysis of Hardy-Weinberg equilibrium population ranged from 0.02 to 0.09, while the highest haplotypes found in swamp bogs (monotonic) (0.9384) then rainfed (0.7111) and tides (0.6). Heterozygosity was found uniquely in the swamp monotonic population (BAAAA) and marsh tides (BAACA) and common in all three ecosystems found in the swampy area (AAABA) . Climbing perch stock divided into two populations monotone and tidal swamp population and rainfed stock. The main concept of genetic conservation is the fitness population where the population is maintained at least 500 tail/region. To increase the genetic diversity of climbing perch, can be done by the introduction of new individuals wich has a higher genetic diversity into the local population, restocking and create reserves of protected areas by the Local Fisheries Authority together with the community around the swampy waters.